entos: A Quantum Molecular Simulation Package

Manby, Frederick R.; Miller, Thomas F.; Bygrave, Peter J.; Ding, Fazhu; Dresselhaus, Thomas; Batista-Romero, Fidel; Buccheri, Alexander; Bungey, Callum; Lee, Sebastian; Meli, Rocco; Miyamoto, Kaito; Steinmann, Casper; Tsuchiya, Takashi; Welborn, Matthew; Wiles, Timothy A.; Williams, Zack

doi:10.26434/chemrxiv.7762646

Cited by 25 publications

(34 citation statements)

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“…All EMFT and GTO-based DFT calculations reported in this study are performed using the entos molecular simulation package (50). These calculations employ standard self-consistent field (SCF) procedures, including use of superposition of the atomic densities (SAD) as the initial guess, the direct inversion in the iterative subspace (DIIS) algorithm for SCF acceleration, and a convergence threshold of 10 -5 a.u.…”

Section: Computational Details 1 Benchmarking the Electronic Structmentioning

confidence: 99%

Imaging covalent bond formation by H atom scattering from graphene

Jiang

Kammler

Ding

et al. 2019

Science

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156

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Viewing the atomic-scale motion and energy dissipation pathways involved in forming a covalent bond is a longstanding challenge for chemistry. We performed scattering experiments of H atoms from graphene and observed a bimodal translational energy loss distribution. Using accurate first-principles dynamics simulations, we show that the quasi-elastic channel involves scattering through the physisorption well where collision sites are near the centers of the six-membered C-rings. The second channel results from transient C–H bond formation, where H atoms lose 1 to 2 electron volts of energy within a 10-femtosecond interaction time. This remarkably rapid form of intramolecular vibrational relaxation results from the C atom’s rehybridization during bond formation and is responsible for an unexpectedly high sticking probability of H on graphene.

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Section: Computational Details 1 Benchmarking the Electronic Structmentioning

confidence: 99%

Imaging covalent bond formation by H atom scattering from graphene

Jiang

Kammler

Ding

et al. 2019

Science

Self Cite

156

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“…In this respect, in 2017 GFN1‐xTB filled a gap in the market of off‐the‐shelf atomistic models as it is fast, robust, reasonably accurate, and works for many metallic systems. It was quickly adapted by the community and implemented in various QC programs like AMS, 18 CP2K, 19 Cuby4, 20 DFTB+, 21 entos, 22 ORCA, 23,24 and TeraChem 25,26 …”

Section: Introductionmentioning

confidence: 99%

Extended tight‐binding quantum chemistry methods

Bannwarth

Caldeweyher

Ehlert

et al. 2020

WIREs Comput Mol Sci

988

964

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This review covers a family of atomistic, mostly quantum chemistry (QC) based semiempirical methods for the fast and reasonably accurate description of large molecules in gas and condensed phase. The theory is derived from a density functional (DFT) perturbation expansion of the electron density in fluctuation terms to various orders similar to the original density functional tight binding model. The term “eXtended” in their name (xTB) emphasizes the parameter availability for almost the entire periodic table of elements (Z ≤ 86) and improvements of the underlying theory regarding, for example, the atomic orbital basis set, the level of multipole approximation and the treatment of the important electrostatic and dispersion interactions. A common feature of most members is their consistent parameterization on accurate gas phase theoretical reference data for geometries, vibrational frequencies and noncovalent interactions, which are the primary properties of interest in typical applications to systems composed of up to a few thousand atoms. Further specialized versions were developed for the description of electronic spectra and corresponding response properties. Besides a provided common theoretical background with some important implementation details in the efficient and free xtb program, various benchmarks for structural and thermochemical properties including (transition‐)metal systems are discussed. The review is completed by recent extensions of the model to the force‐field (FF) level as well as its application to solids under periodic boundary conditions. The general applicability together with the excellent cost‐accuracy ratio and the high robustness make the xTB family of methods very attractive for various fields of computer‐aided chemical research. This article is categorized under: Electronic Structure Theory > Ab Initio Electronic Structure Methods Electronic Structure Theory > Semiempirical Electronic Structure Methods Software > Quantum Chemistry

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“…23 All DFT and EMFT calculations reported here are performed using the entos package. 54 For the B3LYP functional used in the paper, the VWN3 local correlation energy 55 is employed. We employ the density-corrected implementation of the method (DC-EMFT) to 5 prevent unphysical collapse of the electronic density.…”

Section: Methodsmentioning

confidence: 99%

Embedded Mean-Field Theory for Solution-Phase Transition-Metal Polyolefin Catalysis

Chen

Lawniczak

Ding

et al. 2020

J. Chem. Theory Comput.

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Decreasing the wall-clock time of quantum mechanics/molecular mechanics (QM/MM) calculations without sacrificing accuracy is a crucial prerequisite for widespread simulation of solution-phase dynamical processes. In this work, we demonstrate the use of embedded mean-field theory (EMFT) as the QM engine in QM/MM molecular dynamics (MD) simulations to examine polyolefin catalysts in solution. We show that employing EMFT in this mode preserves the accuracy of hybrid-functional DFT in the QM region, while providing up to 20-fold reductions in the cost per SCF cycle, thereby increasing the accessible simulation timescales. We find that EMFT reproduces DFT-computed binding energies and optimized bond lengths to within chemical 1

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entos: A Quantum Molecular Simulation Package

Abstract: We describe the a new molecular simulation package that is designed for ab initio molecular dynamics simulations of molecular and condensed-phase chemical reactions and other<br>processes, with particular focus on mean-field and quantum embedding methods for electronic structure.<br>

Cited by 25 publications

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Imaging covalent bond formation by H atom scattering from graphene

Imaging covalent bond formation by H atom scattering from graphene

Extended tight‐binding quantum chemistry methods

Embedded Mean-Field Theory for Solution-Phase Transition-Metal Polyolefin Catalysis

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